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GeneBe API Showcase

This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.

API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.

Documentation & Advanced Usage

Complete API documentation:docs.genebe.net/docs/api/overview/

Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/

Python client for pandas:pypi.org/project/genebe/

Java CLI for VCF files:github.com/pstawinski/genebe-cli

All tools documented at:docs.genebe.net

API Request Examples for Variant: 7-130367540-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=130367540&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "7",
      "pos": 130367540,
      "ref": "T",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "ENST00000474905.6",
      "consequences": [
        {
          "aa_ref": "L",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "NM_080385.5",
          "protein_id": "NP_525124.3",
          "transcript_support_level": null,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 436,
          "cds_start": 1007,
          "cds_end": null,
          "cds_length": 1311,
          "cdna_start": 1548,
          "cdna_end": null,
          "cdna_length": 1985,
          "mane_select": "ENST00000474905.6",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "S",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "ENST00000474905.6",
          "protein_id": "ENSP00000417314.1",
          "transcript_support_level": 1,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 436,
          "cds_start": 1007,
          "cds_end": null,
          "cds_length": 1311,
          "cdna_start": 1548,
          "cdna_end": null,
          "cdna_length": 1985,
          "mane_select": "NM_080385.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "ENST00000393213.7",
          "protein_id": "ENSP00000376907.3",
          "transcript_support_level": 1,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 436,
          "cds_start": 1007,
          "cds_end": null,
          "cds_length": 1311,
          "cdna_start": 1007,
          "cdna_end": null,
          "cdna_length": 1444,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "ENST00000461828.5",
          "protein_id": "ENSP00000418183.1",
          "transcript_support_level": 1,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 436,
          "cds_start": 1007,
          "cds_end": null,
          "cds_length": 1311,
          "cdna_start": 1490,
          "cdna_end": null,
          "cdna_length": 1794,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "ENST00000485477.5",
          "protein_id": "ENSP00000420237.1",
          "transcript_support_level": 1,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 436,
          "cds_start": 1007,
          "cds_end": null,
          "cds_length": 1311,
          "cdna_start": 2136,
          "cdna_end": null,
          "cdna_length": 2573,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "NM_001127441.2",
          "protein_id": "NP_001120913.1",
          "transcript_support_level": null,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 436,
          "cds_start": 1007,
          "cds_end": null,
          "cds_length": 1311,
          "cdna_start": 1601,
          "cdna_end": null,
          "cdna_length": 2038,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "NM_001318223.2",
          "protein_id": "NP_001305152.1",
          "transcript_support_level": null,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 436,
          "cds_start": 1007,
          "cds_end": null,
          "cds_length": 1311,
          "cdna_start": 1490,
          "cdna_end": null,
          "cdna_length": 1927,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "ENST00000466363.6",
          "protein_id": "ENSP00000419025.2",
          "transcript_support_level": 5,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 436,
          "cds_start": 1007,
          "cds_end": null,
          "cds_length": 1311,
          "cdna_start": 1662,
          "cdna_end": null,
          "cdna_length": 2099,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "NM_001127442.2",
          "protein_id": "NP_001120914.1",
          "transcript_support_level": null,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 403,
          "cds_start": 1007,
          "cds_end": null,
          "cds_length": 1212,
          "cdna_start": 1490,
          "cdna_end": null,
          "cdna_length": 1842,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "ENST00000431780.6",
          "protein_id": "ENSP00000393045.2",
          "transcript_support_level": 2,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 403,
          "cds_start": 1007,
          "cds_end": null,
          "cds_length": 1212,
          "cdna_start": 1452,
          "cdna_end": null,
          "cdna_length": 1803,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
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          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "XM_005250710.2",
          "protein_id": "XP_005250767.1",
          "transcript_support_level": null,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 436,
          "cds_start": 1007,
          "cds_end": null,
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          "cdna_start": 1534,
          "cdna_end": null,
          "cdna_length": 1971,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
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          "exon_count": 12,
          "intron_rank": null,
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          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "XM_005250712.2",
          "protein_id": "XP_005250769.1",
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        {
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          "strand": true,
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          ],
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          "intron_rank": null,
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          "gene_symbol": "CPA5",
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          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "XM_011516698.2",
          "protein_id": "XP_011515000.1",
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          "cds_start": 1007,
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          "cdna_start": 1175,
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        {
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 10,
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          "intron_rank": null,
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          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "XM_011516703.2",
          "protein_id": "XP_011515005.1",
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        {
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          "hgvs_c": "c.1007T>C",
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        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "XM_024447000.2",
          "protein_id": "XP_024302768.1",
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        {
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          "gene_symbol": "CPA5",
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          "hgvs_c": "c.1007T>C",
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        {
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          "gene_symbol": "CPA5",
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        {
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          ],
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        {
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          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser",
          "transcript": "XM_047421037.1",
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        {
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
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          "exon_count": 12,
          "intron_rank": null,
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          "gene_symbol": "CPA5",
          "gene_hgnc_id": 15722,
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        {
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          "hgvs_c": "c.68-870T>C",
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          "transcript": "ENST00000479492.1",
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      ],
      "gene_symbol": "CPA5",
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      "dbsnp": "rs11761888",
      "frequency_reference_population": 0.20608957,
      "hom_count_reference_population": 37055,
      "allele_count_reference_population": 332406,
      "gnomad_exomes_af": 0.202133,
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      "gnomad_genomes_ac": 37099,
      "gnomad_exomes_homalt": 31857,
      "gnomad_genomes_homalt": 5198,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.004091799259185791,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.009999999776482582,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.08,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0606,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.79,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 1.18,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.01,
      "spliceai_max_prediction": "Benign",
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": -12,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BA1",
      "acmg_by_gene": [
        {
          "score": -12,
          "benign_score": 12,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000474905.6",
          "gene_symbol": "CPA5",
          "hgnc_id": 15722,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.1007T>C",
          "hgvs_p": "p.Leu336Ser"
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      ],
      "clinvar_disease": "",
      "clinvar_classification": "",
      "clinvar_review_status": "",
      "clinvar_submissions_summary": "",
      "phenotype_combined": null,
      "pathogenicity_classification_combined": null,
      "custom_annotations": null
    }
  ],
  "message": null
}